SMTL ID : 5e3i.1

Crystal Structure of a Histidyl-tRNA synthetase from Acinetobacter baumannii with bound L-Histidine and ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: R.122, R.130 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain B: R.122, R.130 Ligands: ATP.5 No protein-ligand interaction detected (PLIP)

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 17 residues within 4Å: Chain A: R.122, E.124, G.129, R.130, Y.131, F.134, Q.136, R.268, T.290, V.291, C.292, A.293, M.319, G.320, R.323 Ligands: MG.1, HIS.3 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:E.124, A:Y.131, A:Q.136, A:T.290, A:G.320, A:R.323, A:R.323 Water bridges: A:R.122, A:R.122, A:R.130, A:R.268, A:R.268, A:G.269 Salt bridges: A:R.122, A:R.122, A:R.130, A:R.268, A:R.268, A:R.323 pi-Stacking: A:F.134, A:F.134 pi-Cation interactions: A:R.323 ATP.5: 16 residues within 4Å: Chain B: R.122, E.124, G.129, R.130, Y.131, F.134, Q.136, R.268, T.290, V.291, C.292, A.293, G.320, R.323 Ligands: MG.4, HIS.6 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:E.124, B:Y.131, B:Q.136, B:T.290, B:G.320, B:R.323 Water bridges: B:R.122, B:R.122, B:R.122, B:R.130, B:R.130, B:R.268, B:R.268, B:R.268, B:R.268, B:G.269, B:T.290 Salt bridges: B:R.122, B:R.122, B:R.130, B:R.268, B:R.268, B:R.323 pi-Stacking: B:F.134, B:F.134 pi-Cation interactions: B:R.323

2 x HIS: HISTIDINE(Non-covalent)

HIS.3: 16 residues within 4Å: Chain A: E.92, T.94, R.122, Q.136, E.140, L.270, Y.272, Y.273, A.293, G.294, G.295, Y.297, G.316, F.317, A.318 Ligands: ATP.2 14 PLIP interactions: 12 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:A.318 Hydrogen bonds: A:E.92, A:T.94, A:T.94, A:Q.136, A:Q.136, A:E.140, A:Y.272, A:Y.273, H.3, H.3 Water bridges: A:G.93, A:T.94 Salt bridges: A:R.122 HIS.6: 15 residues within 4Å: Chain B: E.92, T.94, R.122, Q.136, E.140, Y.272, Y.273, A.293, G.294, G.295, Y.297, G.316, F.317, A.318 Ligands: ATP.5 12 PLIP interactions: 11 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:A.318 Hydrogen bonds: B:E.92, B:T.94, B:T.94, B:Q.136, B:E.140, H.6 Water bridges: B:G.93, B:G.93, B:Y.273, B:Y.273 Salt bridges: B:R.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

SSGCID et al., Crystal Structure of a Histidyl-tRNA synthetase from Acinetobacter baumannii with bound L-Histidine and ATP. to be published

Release Date

2015-11-04

Peptides

Histidine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histidine--tRNA ligase